search

IHCC-cohorts / GECKO

Genomics Cohorts Knowledge Ontology
Other
7 stars 3 forks source link

Remove unnecessary annotations from imports #30

Closed beckyjackson closed 3 years ago

beckyjackson commented 3 years ago

Previously, we included all annotations from import modules, but I think this brought in a lot of unnecessary data. The gizmos.extract module has been updated to handle subsets of annotations, so I think it would be good to utilize this feature.

This PR is a proposal to remove unnecessary annotation properties and only include the following from imports:

ID Label
IAO:0000112 example of usage
IAO:0000115 definition
IAO:0000118 alternative term
IAO:0000119 definition source
oboInOwl:hasAlternativeId has_alternative_id
oboInOwl:hasBroadSynonym has_broad_synonym
oboInOwl:hasExactSynonym has_exact_synonym
oboInOwl:hasNarrowSynonym has_narrow_synonym
oboInOwl:hasRelatedSynonym has_related_synonym
rdfs:comment comment
rdfs:label label

The following are the annotation properties removed. I'm happy to add any of these back in if they are relevant.

ID Label
IAO:0000111 editor preferred term
IAO:0000116 editor note
IAO:0000117 term editor
IAO:0000232 curator note
IAO:0000233 term tracker item
IAO:0000234 ontology term requester
obo:UBPROP_0000001 external_definition
obo:UBPROP_0000002 axiom_lost_from_external_ontology
obo:UBPROP_0000003 homology_notes
obo:UBPROP_0000007 has_relational_adjective
obo:UBPROP_0000008 taxon_notes
obo:UBPROP_0000012 external_ontology_notes
oboInOwl:hasOBONamespace has_obo_namespace
oboInOwl:id id
oboInOwl:inSubset in_subset
rdfs:seeAlso see also
mcourtot commented 3 years ago

all looks fine, except maybe the seeAlso which may be useful for xrefs/mapping?

beckyjackson commented 3 years ago

Sure, I'll add that back in!